Extended Data Fig. 5: Fluorophore quenching as a measure of nucleation and growth.

a, Fluorescent labels used a fluorophore-quencher pair placed on the \(5{\prime} \) ends of two modified tiles unique to one shape, where they were colocated, but had no complementary binding domains, ensuring that dimers could not form, and trimers would not closely colocate the fluorophore and quencher. To constrain the pair to be close enough to quench in a well-formed lattice, one of the two tiles had its orientation and crossover position swapped compared to the unmodified tile for the location. b, Positions and types of all fluorophore/quencher pairs available for use. For one sample, one position for each of four types of fluorophores could be chosen, and tile pairs for those locations replaced by their modified counterparts. Thus different samples could probe different arrangements of up to four locations; four arrangements were used in experiments (e.g., in e). c, Expected behavior of fluorophore labels on shapes as one shape nucleates and grows. d, Fluorescence data for non-quenching (fluorophore tile only, orange) and quenching (5 × 5 lattice around fluorophore and quencher tiles, blue) controls for the ATTO647N fluorophore/quencher pair on A. Here, the temperature ramps linearly from 49 °C to 35 °C at a rate of 0.1 °C/min, with all tiles at 50 nM, and each sample has its fluorescence normalized to its maximum value independently. e, An example of fluorescence growth time measurements (Mockingbird; see Supplementary Information section 6.4.9). Each fluorophore signal, in each sample, is independently normalized to its maximum value during the experiment, and the time between the point where the signal goes below 0.9 (‘10% quenching’) and the end of the experiment is measured (‘growth time’). These times are then summed for all fluorophores, in all four samples, on each shape, resulting in a growth time for each shape, and, when normalized to the sum of all growth times, a relative growth time for each shape. See Methods and Supplementary Information section 3 for design and characterization of the fluorescence readout method, as well as an estimate of the melting temperature of H.